Shrimp health is largely impacted by water quality and the diversity of the microbial populations in the rearing water. Microbes that colonize the shrimp come from the rearing water and sediment. Evidence suggests that environmental factors affect these microbial communities. The shrimp microbiota impacts the development and growth of the organism, the immune system, nutrition and metabolic processes, and the inhibition of pathogenic bacteria. Pathobiome describes the concept that microbial communities interact with the host with the result being either beneficial or harmful.
We have initiated long-term studies of the microbiomes of shrimp pond water with and without disease and with and without treatment. The water microbiome evolves with the changes in the water quality and the microbial species diversity responds to environmental pressures. Our goal is to collect microbiome data from infected ponds, to study the microbial diversity throughout the disease, and to determine triggers for dysbiosis from changes in the microbial content in the rearing pond. This knowledge would allow the development of treatment regimens to reinstate microbial diversity in the pond and the shrimp.
Previously we confirmed WFS infection in two ponds that were at different stages of disease. Microbes from the pond water were collected on filters, DNA was isolated from each pond sample and sent to Charles River Microbial Solution Services for their TAS NGS-based bacterial Identification by targeted amplicon 16S/ITS sequencing (NGS-TAS-16S-20). In 2024, we reported the top ten microbes identified from each pond with conclusions from this data limited.
Subsequently we obtained the full data set with 186,572 reads for Pond A2 and 217,302 reads for Pond A4 with 57% of the reads classified for both samples. The ponds exhibited a similar background of microbes; Pond A2 had 15 Phyla and Pond A4 had 21 Phyla represented in their bacteria populations. The similarity in microbes is not surprising because the ponds were from the same farm, shared the same water supply, contained the same shrimp species, and had the same farming practices. The Phyla that represented over 1% of the microbial population in both ponds were Bacteroidota, Chloroflexota, Cyanobacteriota, Planctomycetota, Pseudomonadota (synonym Proteobacteria), and Actinomycetota. Actinomycetota and Proteobacteria had a high percentage of reads from both ponds. However, Pond A2 with the severe infection had about half the number of Actinomycetota as Pond A4, (21% and 45.60% respectively) while Pond A2 had almost twice the number of Proteobacteria (45.725% and 25.95%).